Applications and Efficiencies of the First Cat 63K DNA Array Wesley C
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Washington University School of Medicine Digital Commons@Becker Open Access Publications 2018 Applications and efficiencies of the first cat 63K DNA array Wesley C. Warren Washington University School of Medicine in St. Louis Follow this and additional works at: https://digitalcommons.wustl.edu/open_access_pubs Recommended Citation Warren, Wesley C., ,"Applications and efficiencies of the first cat 63K DNA array." Scientific Reports.8,. 7024. (2018). https://digitalcommons.wustl.edu/open_access_pubs/7595 This Open Access Publication is brought to you for free and open access by Digital Commons@Becker. It has been accepted for inclusion in Open Access Publications by an authorized administrator of Digital Commons@Becker. For more information, please contact [email protected]. www.nature.com/scientificreports Correction: Author Correction OPEN Applications and efciencies of the frst cat 63K DNA array Barbara Gandolf1, Hasan Alhaddad2, Mona Abdi2, Leslie H. Bach3,4, Erica K. Creighton1, Brian W. Davis 5, Jared E. Decker 6, Nicholas H. Dodman7, Jennifer C. Grahn3,8, Robert A. 3,8 9 10 3,11 12 Received: 17 October 2017 Grahn , Bianca Haase , Jens Haggstrom , Michael J. Hamilton , Christopher R. Helps , Jennifer D. Kurushima3,13, Hannes Lohi14, Maria Longeri15, Richard Malik16, Kathryn M. Meurs17, Accepted: 16 April 2018 Michael J. Montague 18, James C. Mullikin 19, William J. Murphy5, Sara M. Nilson6, Published online: 04 May 2018 Niels C. Pedersen20, Carlyn B. Peterson3, Clare Rusbridge21, Rashid Saif22, G. Diane Shelton23, Wesley C. Warren24, Muhammad Wasim25 & Leslie A. Lyons1 The development of high throughput SNP genotyping technologies has improved the genetic dissection of simple and complex traits in many species including cats. The properties of feline 62,897 SNPs Illumina Infnium iSelect DNA array are described using a dataset of over 2,000 feline samples, the most extensive to date, representing 41 cat breeds, a random bred population, and four wild felid species. Accuracy and efciency of the array’s genotypes and its utility in performing population-based analyses were evaluated. Average marker distance across the array was 37,741 Kb, and across the dataset, only 1% (625) of the markers exhibited poor genotyping and only 0.35% (221) showed Mendelian errors. Marker polymorphism varied across cat breeds and the average minor allele frequency (MAF) of all markers across domestic cats was 0.21. Population structure analysis confrmed a Western to Eastern structural continuum of cat breeds. Genome-wide linkage disequilibrium ranged from 50–1,500 Kb for domestic cats and 750 Kb for European wildcats (Felis silvestris silvestris). Array use in trait association mapping was investigated under diferent modes of inheritance, selection and population sizes. The efcient array design and cat genotype dataset continues to advance the understanding of cat breeds and will support monogenic health studies across feline breeds and populations. 1Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri - Columbia, Columbia, MO, USA. 2Department of Biological Sciences, Kuwait University, Safat, Kuwait. 3Department of Population Health and Reproduction, School of Veterinary Medicine, University of California – Davis, Davis, CA, USA. 4University of San Francisco, San Francisco, CA, USA. 5Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA. 6Division of Animal Sciences, University of Missouri - Columbia, Columbia, MO, USA. 7Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA, USA. 8Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California - Davis, Davis, CA, USA. 9Sydney School of Veterinary Science, University of Sydney, Sydney, Australia. 10Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden. 11Department of Biochemistry, University of California – Riverside, Riverside, CA, USA. 12Langford Vets, University of Bristol, Bristol, United Kingdom. 13Foothill College, Los Altos Hills, CA, USA. 14Department of Veterinary Biosciences, Research Programs Unit, Molecular Neurology, University of Helsinki, and The Folkhalsan Institute of Genetics, Helsinki, Finland. 15Department of Veterinary Medicine, Università degli Studi di Milano, Milan, Italy. 16Centre for Veterinary Education, University of Sydney, New South Wales, Australia. 17Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA. 18Department of Neuroscience, Parelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. 19NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA. 20Center for Companion Animal Health, School of Veterinary Medicine, University of California - Davis, Davis, CA, USA. 21School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey, United Kingdom. 22Institute of Biotechnology, Gulab Devi Educational Complex, Lahore, Pakistan. 23Department of Pathology, University of California, San Diego, La Jolla, CA, USA. 24McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA. 25Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, Pakistan. Barbara Gandolf and Hasan Alhaddad contributed equally to this work. Correspondence and requests for materials should be addressed to H.A. (email: hhalhaddad@ gmail.com) or L.A.L. (email: [email protected]) SCIENTIFIC REPORTS | (2018) 8:7024 | DOI:10.1038/s41598-018-25438-0 1 www.nature.com/scientificreports/ Feral and owned cats are collectively referred to as “domestic cats”. Over 88 million domestic cats live in homes in the USA alone1,2, and are valued companions, providers of vermin control, and important biomedical models3. Te domestic cat, Felis silvestris catus, represents one of the ~41 species in the family Felidae4–6 with the extant species having a common ancestor ~11 million years ago7,8. Previous archeological and genetic research has suggested the modern domesticated cat descends from at least one wildcat progenitor subspecies, Felis silvestris libyca, around 10,000 years ago9–11. Agricultural development is thought to be the key event that initiated and infuenced the domestication of the cat11–13. Te availability of grains and other food sources in and around areas of human settlements resulted in sub- stantial rodent population expansion, which in turn attracted the natural predator, the progenitor of the domestic cat, from the wildcat population. Over time, individual cats with temperaments suitable for co-habitation with human populations became isolated from the wild counterparts and evolved into the semi-domesticated cat of today. In spite of their rapid spread and isolation from the progenitor populations, domestic cats have remained remarkably similar to their felid cousins (Felis silvestris subsp.) in form and behavior12,14 and these wild popula- tions have remained widespread across the Old World. Te establishment of cat breeds from domesticated and tamed free-roaming cat populations is a relatively recent event. Many domesticated animal species such as cattle, goats, pig, dog, and horse, were selected for traits of economic value such as meat, milk, drought tolerance, endurance, strength, protection, hunting ability, speed and metabolic efciency from the onset of their domestication15,16. All these desired qualities are the products of hundreds to thousands of years of selective breeding12,13. However, the domestic cat breeds were selectively bred primarily for aesthetically pleasing traits such as coat color, length, and texture, most of which occurred only in the past 150 years17,18. Between 40 and 55 diferent cat breeds are currently recognized for standardized phenotypic characteristics by worldwide cat fancy associations, including the Cat Fanciers’ Association19, Te International Cat Association20, the Governing Council of the Cat Fancy21, Federation International Feline22, and the World Cat Federation23,24. Due to inbreeding, many cat breeds harbor heritable diseases that are important biomedical models for human health (http://omia.angis.org.au/home/)3,25. However, owned random-bred and un-owned or semi-owned feral cats represent the overwhelming majority of cats in the world26. Te continued development and progress of genetic resources for humans have transformed the feld of genetics and accelerated the rate of scientifc discovery27–29. Similarly, genetic resources for the domestic cat have methodically and systematically been developed, which include somatic cell hybrid panels30,31, radiation hybrid maps32–39, genetic linkage maps40–44, and the sequencing of the cat genome45–48. Feline genome sequencing eforts to date have included: (1) a 1.9x draf sequence as a representative of the family Felidae45, (2) additional light sequencing (~1X coverage) of six individuals from several breeds and an African wild cat (Felis silvestris cafra) for SNPs discovery47, (3) high throughput sequencing of four pooled samples from each of six diferent domestic cat breeds, wildcats, as well as the reference cat genome46 and (4) a high-resolution SNP array-based linkage map that supported the assembly of Felis_catus v8.048. Te SNPs discovered via these sequencing eforts were used to con- struct an Illumina Infnium iSelect 63K DNA cat array. Te produced array contains